RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.t8rxHD/RM_1847.WedJun260925402024 Search Engine = rmblast 2.13.0+ Threads = 32 Dependencies: TRF 4.09, RECON , RepeatScout 1.0.6, RepeatMasker 4.1.4 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1719419140 Database = /dev/shm/rModeler.t8rxHD/GCF_029289425.2_NHGRI_mPanPan1-v2.0_pri - Sequences = 31 - Bases = 3244905271 Storage Throughput = excellent ( 1062.53 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40040976 bp ( 40000974 non ambiguous ) - Num Contigs Represented = 26 - Sequence extraction : 00:01:41 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:17 (hh:mm:ss) Elapsed Time Round Time: 00:32:19 (hh:mm:ss) Elapsed Time : 238 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11857 repeats masked totaling 2684843 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000111 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10000111 bp After Masking: 6188968 bp Masked: 38.11 % -- Input Database Coverage: 10000111 bp out of 3244905271 bp ( 0.31 % ) Sampling Time: 00:04:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:07 (hh:mm:ss) Elapsed Time, 5810 HSPs Collected Number of families returned by RECON: 805 Round Time: 00:09:35 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 39063 repeats masked totaling 8766046 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30040785 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 30000783 bp After Masking: 17807846 bp Masked: 40.64 % -- Input Database Coverage: 40040896 bp out of 3244905271 bp ( 1.23 % ) Sampling Time: 00:16:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:25:41 (hh:mm:ss) Elapsed Time, 29596 HSPs Collected Number of families returned by RECON: 2572 Round Time: 00:42:58 (hh:mm:ss) Elapsed Time : 82 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:33:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 127773 repeats masked totaling 29425542 bp(s). - TE Masking time 00:01:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90162069 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 90002060 bp After Masking: 50759038 bp Masked: 43.60 % -- Input Database Coverage: 130202965 bp out of 3244905271 bp ( 4.01 % ) Sampling Time: 00:38:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 02:46:10 (hh:mm:ss) Elapsed Time, 93518 HSPs Collected Number of families returned by RECON: 7852 Round Time: 03:29:01 (hh:mm:ss) Elapsed Time : 182 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:48:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 431069 repeats masked totaling 96062197 bp(s). - TE Masking time 00:06:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270535214 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 270015175 bp After Masking: 143202590 bp Masked: 46.96 % -- Input Database Coverage: 400738179 bp out of 3244905271 bp ( 12.35 % ) Sampling Time: 02:07:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22879230 Comparison Time: 21:12:53 (hh:mm:ss) Elapsed Time, 417280 HSPs Collected Number of families returned by RECON: 28940 Round Time: 23:50:22 (hh:mm:ss) Elapsed Time : 397 families discovered. RepeatScout/RECON discovery complete: 914 families found Classification Time: 00:41:44 (hh:mm:ss) Elapsed Time Program Time: 29:25:59 (hh:mm:ss) Elapsed Time